[3dem] Local Resolution

Benjamin Himes himes.benjamin at gmail.com
Mon Jun 11 16:27:03 PDT 2018


Hi Jillian & Reza,

The figures in the paper that Mohsen linked to, reflect what seems to be a
general consensus - displaying the local resolution on a scale akin to a
heat map, with higher temperature colors corresponding to higher
temperature factors (lower resolution.)

The scale bar proximal to your map is nice, and I would add that you should
probably make sure that this scale reflects the full resolution range
examined by your local resolution program of choice. It seems common to see
a map where many of the reported resolution values are piled up at one end
or the other of this range, which to me at least, seems worrisome.

Just my opinion,

HTH,

Ben

------------------------
Benjamin Himes

cryoEM methods development
Grigorieff lab
<https://mail.hhmi.org/owa/redir.aspx?C=SbsCefkcbOt75jDyr05lpd3OifVN_utmfvnhZrtXS7Bl2i2eOXXVCA..&URL=http%3a%2f%2fgrigoriefflab.janelia.org%2f>,
HHMI Janelia Research Campus

cryoSTAC development @ emClarity
<https://mail.hhmi.org/owa/redir.aspx?C=8yDzXj54yTidMevTB7q5m3liEVwqAZ9LxuXQ4iYOVvtl2i2eOXXVCA..&URL=https%3a%2f%2fgithub.com%2fbHimes%2femClarity%2fwiki>

-------------------------

On Mon, Jun 11, 2018 at 6:32 PM, <3dem-request at ncmir.ucsd.edu> wrote:

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> Today's Topics:
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>    1. Local resolution image (Reza Khayat)
>    2. Re: Local resolution image (Jillian Chase)
>    3. Re: Local resolution image (Mohsen Kazemi)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 11 Jun 2018 20:58:00 +0000
> From: Reza Khayat <rkhayat at ccny.cuny.edu>
> To: "CCPEM at JISCMAIL.AC.UK" <CCPEM at JISCMAIL.AC.UK>,
>         "3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>
> Subject: [3dem] Local resolution image
> Message-ID: <da6fed29a0fc4c2e871cc544a706bfce at CCNY-MBX2.itcs.ccny.lan>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi,
>
> Has a standard been established in the field for coloring local resolution
> maps? If not, are there any suggestions (i.e. FSC resolution is blue, 2x
> FSC resolution is white, and 4x FSC resolution is red). Thanks.
>
> Best wishes,
> Reza
>
> Reza Khayat, PhD
> Assistant Professor
> Department of Chemistry
> City College of New York
> 85 Saint Nicholas Terrace, CDI 2.318
> New York, NY 10031
> http://www.khayatlab.org/
> 212-650-6070
>
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> ------------------------------
>
> Message: 2
> Date: Mon, 11 Jun 2018 17:55:26 -0400
> From: Jillian Chase <jillian.d.chase at gmail.com>
> To: Reza Khayat <rkhayat at ccny.cuny.edu>
> Cc: "3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>,
>         "CCPEM at JISCMAIL.AC.UK" <CCPEM at JISCMAIL.AC.UK>
> Subject: Re: [3dem] Local resolution image
> Message-ID: <FA69B6DA-E4A8-49F3-901A-EDAD8AF9A172 at gmail.com>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi All,
>
> I'm also very curious about this- has any standard been implemented? It
> would be nice to have a general guideline so reported data is more-or-less
> equally easy to interpret in various papers.
>
> We are in the process of drafting a manuscript and have gone back and
> forth about how to show local resolution in an intuitive way. Some areas of
> our map are better or worse than the global resolution. What we've settled
> on (for now) is a rainbow color spectrum (Chimera) in which the range spans
> both above and below our global res and we have included the scale next to
> our map colored by res and labeled with resolution. Is there a universal
> standard that the community is moving towards for this or are we
> approaching it correctly (or as best we can) for now?
>
> Any insight would be very useful.
>
> All the best,
> Jillian
>
> Jillian Chase
> PhD Candidate, Jeruzalmi Lab
> CUNY/CCNY
>
> > On Jun 11, 2018, at 4:58 PM, Reza Khayat <rkhayat at ccny.cuny.edu> wrote:
> >
> > Hi,
> >
> > Has a standard been established in the field for coloring local
> resolution maps? If not, are there any suggestions (i.e. FSC resolution is
> blue, 2x FSC resolution is white, and 4x FSC resolution is red). Thanks.
> >
> > Best wishes,
> > Reza
> >
> > Reza Khayat, PhD
> > Assistant Professor
> > Department of Chemistry
> > City College of New York
> > 85 Saint Nicholas Terrace, CDI 2.318
> > New York, NY 10031
> > http://www.khayatlab.org/
> > 212-650-6070
> >
> > _______________________________________________
> > 3dem mailing list
> > 3dem at ncmir.ucsd.edu
> > https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem
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> ------------------------------
>
> Message: 3
> Date: Mon, 11 Jun 2018 22:32:22 +0000
> From: Mohsen Kazemi <mohsen.kazemi at unimelb.edu.au>
> To: Jillian Chase <jillian.d.chase at gmail.com>, Reza Khayat
>         <rkhayat at ccny.cuny.edu>
> Cc: "3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>,
>         "CCPEM at JISCMAIL.AC.UK" <CCPEM at JISCMAIL.AC.UK>
> Subject: Re: [3dem] Local resolution image
> Message-ID:
>         <SYBPR01MB3692C97AE7C2D9622195A39BC3780 at SYBPR01MB3692.
> ausprd01.prod.outlook.com>
>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Jillian and Reza,
>
> This paper should have some useful answers for you;
> https://www.ncbi.nlm.nih.gov/pubmed/29395788. It introduces a method to
> calculate local resolution ?MonoRes? by J. Vilas et al (Structure, 2018).
> They propose a fully automatic and accurate method to determine the local
> resolution of 3D map. And, the method is available in the Scipion.
>
> Cheers,
> Mohsen
> --
> Mohsen Kazemi, PhD, PEng
> Postdoctoral Research Fellow
>
> Department of Biochemistry and Molecular Biology
> School of Biomedical Sciences
> Faculty of Medicine, Dentistry and Health Sciences
> The University of Melbourne
> Room 363, David Penington Building (Bio21 Institute), 30 Flemington Rd,
> Parkville, VIC 3052, Australia
>
> Phone : +61 3 834 40285
> Email  : mohsen.kazemi at unimelb.edu.au<mailto:mohsen.kazemi at unimelb.edu.au>
>               mohsenkazemi20 at gmail.com<mailto:mohsenkazemi20 at gmail.com>
>
> From: 3dem <3dem-bounces at ncmir.ucsd.edu> On Behalf Of Jillian Chase
> Sent: Tuesday, June 12, 2018 7:55 AM
> To: Reza Khayat <rkhayat at ccny.cuny.edu>
> Cc: 3dem at ncmir.ucsd.edu; CCPEM at JISCMAIL.AC.UK
> Subject: Re: [3dem] Local resolution image
>
> Hi All,
>
> I'm also very curious about this- has any standard been implemented? It
> would be nice to have a general guideline so reported data is more-or-less
> equally easy to interpret in various papers.
>
> We are in the process of drafting a manuscript and have gone back and
> forth about how to show local resolution in an intuitive way. Some areas of
> our map are better or worse than the global resolution. What we've settled
> on (for now) is a rainbow color spectrum (Chimera) in which the range spans
> both above and below our global res and we have included the scale next to
> our map colored by res and labeled with resolution. Is there a universal
> standard that the community is moving towards for this or are we
> approaching it correctly (or as best we can) for now?
>
> Any insight would be very useful.
>
> All the best,
> Jillian
>
> Jillian Chase
> PhD Candidate, Jeruzalmi Lab
> CUNY/CCNY
>
> On Jun 11, 2018, at 4:58 PM, Reza Khayat <rkhayat at ccny.cuny.edu<mailto:
> rkhayat at ccny.cuny.edu>> wrote:
> Hi,
>
> Has a standard been established in the field for coloring local resolution
> maps? If not, are there any suggestions (i.e. FSC resolution is blue, 2x
> FSC resolution is white, and 4x FSC resolution is red). Thanks.
>
> Best wishes,
> Reza
>
> Reza Khayat, PhD
> Assistant Professor
> Department of Chemistry
> City College of New York
> 85 Saint Nicholas Terrace, CDI 2.318
> New York, NY 10031
> http://www.khayatlab.org/<http://www.khayatlab.org/>
> 212-650-6070
>
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